Instructions ProMol Project Homology Models    v2
12/3/12
VDS

See: http://vdsstream.wikispaces.com/ProMol+Project

Purpose: make homology models for our enzymes that need them. We will use the ICM program on the DDFE because it seems to do a better job than just the SWISS-Model alone. 

Use SWISS-Model to predict template
	go to:  
	http://swissmodel.expasy.org/
	Choose Tools >> Template Identification:
	Input a Project Title:  e.g.  "Lmajor Template"
Copy and paste the Amino Acid sequence of the protein (can get from the Targets page on Wikispaces)
	Leave the defaults for the rest
	Wait. 
	Copy down the 4 digit PDB identifier for the Model. 
		Type this into the Wikispaces page too. 
	Download the actual PDB file for the template
	You will copy this over to the DDFE

Start up DDFE connection (WinSCP or SSH)
On DDFE make a folder of the name of the organism (e.g. Lmajor, Wbm, FtHap, YEPTP, Tbrucei, PfDXR, SAgalactiae, Lmonocytogenes): 
	/OrganismName      (e.g. /Lmajor)
	Make a folder within that called: 
	/OrganismName/ICMmodel		(e.g. /Lmajor/ICMmodel)
	Copy the template PDB file into this folder


Use ICM to create homology itself
	Open Xming, XLaunch, then Putty
	Then go to the folder that you just made
	Type   $icm &    at the command prompt. 
	
	Use sequence of Target Protein for amino acid 
	Have to go to File >> New >> Sequence  and paste in the sequence. 
	Then Extract sequence of Template (right click)
	Use template PDB  that was found in SWISSmodel template search.

	Select BOTH sequences in workspace, Right Click and ALign
	
	Save your ICM project    File >> Save Project As >> ???.icb
	Homology >> Build Model
	Do NOT Display resutls
	Minimize side chains
	Sample side chains
	Do NOT write object to file

	When it is done, a new ICM Object will be made. Right Click on it and Save As >> pdb (*.ent)
	** note This is tricky - Make Sure only the protein name is highlighted and not the Sequence beneath it. Otherwise you won't see the Save As pdb(*.ent) option.

	Save your ICM project again    File >> Save Project As >> ???.icb


COMPARE QUALITY OF STRUCTURES USING MOLPROBITY
	ICMmodel vs. Template

Transfer your .ent model file to your local computer

Do Molprobity on template .pdb 
	-- don't add FLIPS, Do add H's,
Save a copy of the Molprobity output as HTML file (be sure to only do the 'single-page' HTML file) 

Do Molprobity on .ent file from ICMmodel
	Save a copy of the Molprobity output as HTML file (be sure to only do the 'single-page' HTML file) 
-- don't add FLIPS, Do add H's,

Transfer files to DDFE for storage
Transfer file to Google Docs/ProMolProject for storage and review
	
On the Wikispaces page of ProMol Project
	enter the Molprobity scores for both the Template and the Model
Template: Clash score, Molprobity score = ???, ???
Model: Clash score, Molprobity score = ???, ???







